On Friday, a new Covid-19 variant first identified in southern Africa was revealed, and by Saturday, the World Health Organization (WHO) had named it Omicron and declared it a “variant of concern”. This is because it carries a high number of mutations on its spike protein linked with increased transmissibility, and which may decrease the effectiveness of measures such as vaccinations and treatments.
By Sunday, two Omicron cases were confirmed in Australia, where the government promptly slammed the border shut to travellers from nine African nations. So how worried should Australia be about Omicron, and when will we know more about it?
The speed Omicron is being studied should give us comfort
Prof Stuart Turville heads the Kirby Institute’s ‘containment lab’ at the University of New South Wales, where the virus is grown in many of its mutations. This week, his team will begin growing Omicron. By the weekend, he hopes the virus will have bloomed, and they can test how effectively antibodies bind to it, taken from all different kinds of patients.
“In early 2020 it would take us about a month in the lab to understand how well antibodies bind to it and how ‘fit’ the virus is,” Turville said. “Now, we can get that information within a week.”
Turville’s team will test how the virus behaves against antibodies from vaccinated patients; antibodies from people who are recovered and vaccinated; and antibodies from people who are sick and vaccinated. They will also work with other research institutes to test how the virus responds to therapeutics like hyperimmune globulin, an antibody-rich therapy developed using plasma donations.
Prof Sharon Lewin is a world-renowned infectious diseases expert and the director of the Doherty Institute in Melbourne, which provides pandemic modelling to the federal government. She predicts the mutations Omicron carries will have the greatest interference with the antibody treatments being used to treat Covid patients, while vaccines will remain effective.
“They’re very sensitive to spike protein mutations,” she said. “But vaccine-induced antibodies have a bit of tolerance for variation in the virus. The vaccines that we designed worked really well against Delta.”
She added that the protection vaccines offer against hospitalisation and death may be due to other parts of the immune system than antibodies, such as T-cells, which attack invading pathogens. “T-cells target all parts of the virus, not just the spike protein. Vaccinated people may well have T-cells that can do a pretty good job at protecting against variants,” Lewin said.
What is Australia hoping to learn about Omicron?
It takes time to see how a virus behaves in the real world, including new variants. While Omicron has been identified in about a dozen countries to date, including South Africa, the UK, Israel and Australia, the numbers are too low to see if it is overtaking Delta and if it is, if that is due to the mutations.
Most cases are in South Africa, where the World Health Organization says Omicron infections are increasing steeply.
Because Australia is not swamped with Omicron patients or Covid-19 cases generally, sequencing can be performed in the laboratory for every person in quarantine who tests positive to it.
“Yes, the lab isn’t the real world but it’s a really good early-warning signal and surrogate for the real world, and it can be the first line of evidence we have after seeing something that’s not quite right in the real world,” Turville said.
“Epidemiological efforts, such as understanding the disease severity in people who are both vaccinated and unvaccinated is very important. We learn a lot from watching it spread in the community. But that data can take two-to-three months to tell us enough.”
How worried should we be about Omicron in Australia?
The health minister, Greg Hunt, said on Monday the federal government had asked the Australian Technical Advisory Group on Immunisation to examine whether third “booster” vaccine shots should be brought forward to sooner than six months.
But he said there was no strong evidence yet that Omicron evades vaccines, and given Australia has a high vaccine coverage this will offer strong protection. Even if Omicron does prove to evade vaccines, Pfizer can tweak the mRNA vaccine within six weeks and ship initial batches within 100 days.
“We’re well-prepared and we are in the best scientific hands in the world,” Hunt said.
However, the arrival of Omicron has raised concerns about vaccine equity, with most of Africa having very poor vaccination rates while Australia rolls out third doses. There have been calls for countries like Australia to do more to increase global vaccine supply.
We must not get ahead of ourselves
Lewin said “maybe we need to rethink” the WHO classification system, given WHO had labelled Omicron a “variant of concern” in the absence of enough evidence that it is more transmissible or evading vaccines.
Other factors may have led to it spreading rapidly, for example, if it got into highly vulnerable populations. It could also be due to chance.
“The WHO chose to press that ‘variant of concern’ button very early, after seeing a new strain rapidly replace Delta in South Africa and assumed therefore it must be more transmissible,” she said.
“But once you push that button, it creates chaos around the world. We should only be ramping up our response dramatically, including closing borders, if there is a real variant of concern, meaning it’s causing more severe disease or deaths and evading the immune response. We don’t know all that yet. As a global community we need to think about what this means when we identify a variant of concern, because we don’t really have an agreed plan.”
Lewin said she was concerned border closures punished countries with excellent surveillance systems like South Africa. She said variants always find their way in eventually, with Delta coming into Australia even with international border closures. There could be other highly mutated forms of the virus that had not been detected, she said.
“You can’t keep a variant out, she said. [Omicron] may well be in northern Africa and we don’t know about it … many parts of Africa and many other countries don’t have a really good surveillance system.”